Image Tutorial: Opened Interface

This tutorial describes how to reveal an interface by splaying it open
like a book. The structures are shown as surfaces with interactive shadows.
See also:
Intersurf,
presets,
tips on preparing images

The structure contains porcine pancreatic trypsin, chain A,
complexed with a trypsin inhibitor from soybean, chain B.
Move and scale (zoom)
with the mouse to see how the two proteins fit together.
Resize the window as desired, either by dragging its lower right corner
with the mouse or by using the command
windowsize.
The window dimensions define the aspect ratio (width:height)
of output images, but image resolution
can be specified independently when an image is saved.
An 800x500-pixel window was used for the example images at right.

In chain B, there is a break in the ribbon and a dashed line
where atomic coordinates could not be resolved.
Hide this dashed line “pseudobond” and split the model
to facilitate moving chains independently:

You can save/restore multiple positions using different names,
and positions are included in subsequently saved
session files.
To save your work at any point, save a
session (see the File menu).

To open the interface, we will:

orient the complex so that trypsin (green) is on the left and the
inhibitor (purple) is on the right, with the interface approximately edge-on

rotate each protein 90° so that its interface surface
is facing the viewer

translate the proteins apart horizontally

The first step will be done with the
mouse, but we will create command aliases for the other two since
they may be done many times starting from different initial orientations.
To avoid typing long commands, you can copy text from this page
and paste it into the Command Line:

**These aliases assume the complex is oriented so that #0.1 (trypsin, green)
is on the left and #0.2 (inhibitor, purple) is on the right.**
Aliases can be used in the Command Line, and face-me also appears
in the Aliases menu; separate does not, because it requires
also entering the distance of separation (Å).
The “^” symbol means the alias should only be expanded when
it appears at the beginning of a command.
In the independent rotation mode,
each model rotates about its own center rather than a single collective center.

Before using the aliases, generate initial positions by moving the complex
with the mouse.
If you have already separated the proteins and/or rotated them independently,
first put the complex back together, for example:

The default position is that without user-applied rotations and
translations, as when the structures were first opened.
For using the aliases, a good initial position of the complex
has trypsin on the left and the inhibitor on the right,
with the interface approximately edge-on
(similar to the top image above, but could be
rotated differently about the horizontal axis).
When you have what seems to be a good initial position, save it,
use the aliases to open the interface, and save the open position.
For example:

You can start over by resetting to the closed position
(or whatever you named it).
An existing position can be overwritten by saving to the same name.
However, don't worry about optimizing the positions for figures yet.
The goal at this stage is to simplify opening/closing the interface
to evaluate colorings.

Any one of the following three methods could be used to identify and color
the binding interface.
Remember to put the structures in the bound state (closed-interface position)
before running calculations, and if trying different methods or parameter
values, recoloring the proteins between trials
as in the setup. Previous commands can be
re-executed using the command history.
(Advanced users may be interested in some additional
aliases
used during tutorial development.)
Reset to an open-interface position to see the coloring results.

In the findclash command,
the overlap and hb parameters are adjustable,
with values of 0.0-(–1.0) Å and 0.0 Å, respectively,
recommended for finding contacts.
An overlap cutoff of –1.0 identifies pairs of atoms
with VDW surfaces up to 1.0 &Aring apart. When the command is instead
used to find only clashes (unfavorable, too-close contacts),
hb values > 0.0 help to exclude H-bonding atom pairs.
The two sets of atoms are specified with model numbers
(e.g.#0.1), but chain identifiers could have been used
instead (e.g.:.a), and if water had not been deleted,
the calculation could have been limited explicitly to protein
(e.g.#0.1&protein or :.a&protein).

The total buried area and details of the calculation are given in the
Reply Log.
Different cutoff values could be used, but in this case, atoms with
> 1.0 Å2 of solvent-excluded surface area buried
in the interface are similar to the set of atoms found in the
method 1 example.
Although solvent, ions, and ligands are not enclosed in the displayed
surfaces, the buried-area calculation will include all specified atoms.
Thus it is important to specify only the intended atoms; for example,
if nonprotein atoms were present:

These commands identify where the surfaces are within 2.5 Å of each other.
Again, different cutoffs could be used, but 2.5 gave a result roughly similar
to the preceding examples. The specifications in the contact-area command
(e.g.#0.1) refer to the surface models, which happen to have
the same model numbers as the corresponding atomic structures.

Start the Side View
(under Favorites in the menu)
and place it beside the Chimera window so that you can see the structure
from two directions at once.
By default, Chimera uses perspective, in which nearer parts of structures
appear larger. This enhances 3D perception, but subtly distorts structures
as the eye proceeds from the center of the Chimera window towards the edges.
The orthographic projection (no perspective) may be
better for certain images such as side-by-side comparisons:

Continue translating, rotating, and zooming
with the mouse,
saving and resetting positions, and using the aliases to generate
final views. Starting from a position with the intact complex,
the face-me alias should only be used once, since
it applies a 90° rotation to open the interface.
However, it is fine to use separate multiple times,
or scale or translate the view as a whole
using the mouse (carefully!)
and/or commands, for example:

It is prudent to save your favorite views as positions, then save a session
(and save a session again after incorporating any
finishing touches).
You can overwrite an existing position or session by using the same name.

Many different visual effects can be applied, and choosing which to apply
depends on both personal taste and what the image is meant to illustrate.
The example images above
were made with smooth molecular surfaces, a white background, and shadows:

The result shows a predominantly positive protuberance on the inhibitor
(right) interacting with a primarily negative pocket on the enzyme (left),
with the opposite charge pattern on surrounding areas.

To color by per-residue concavity/convexity, open the
Attribute
Calculator (Tools... Structure Analysis... Attribute Calculator).
Calculate a new attribute named convexity for residues
using the Formula

residue.areaSAS/residue.areaSES

Values of convexity
> 1 represent convex areas, while values < 1 represent concave areas.
Click OK to perform the calculation and assignment.
A warning message will appear because some residues have an
areaSES of zero, resulting in a divide-by-zero error.
However, just close the warning dialog; values have been assigned correctly
to the remaining residues. The coloring command could be something like:

The result mainly serves to emphasize what is already evident from the
shadowed surfaces: that a knobby protuberance on the inhibitor
plugs into a socket on trypsin.
The Attributes tutorial, part 2
describes showing per-atom rather than per-residue convexity, but the
results are similar.